Hi,
Thanks a lot for your reply.
So, for the diffusion to structural, I used epi-reg.
epi_reg --epi=<EPI image> --t1=<T1 image> --t1brain=<skull-stripped T1 image> --out=<output matrix>
Then I converted the output using convert xfm to get a structural to DTI matrix.
At this point, can I use the applywarp command as follows:
applywarp -i <mask> -o <output image> -r <DTI image> --postmat=<converted mat. file
Is this correct?
Or should I use flirt for linear registration? Also, since this is seed-based analysis, do I need to register a whole brain atlas to the brains so that it knows where the connections of my region of interest are or not?
Another question: What is the best way to analyze this data afterwards? Probabilistic track? I am doing seed-based analysis and would like to apply the same mask to the resting fMRI data I have afterwards. What do you recommend?
Thanks again and look forward to your reply.
|